Header list of 1iyf.pdb file
Complete list - b 23 2 Bytes
HEADER LIGASE 13-AUG-02 1IYF
TITLE SOLUTION STRUCTURE OF UBIQUITIN-LIKE DOMAIN OF HUMAN PARKIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PARKIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN;
COMPND 5 EC: 6.3.2.19;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P3
KEYWDS UBIQUITIN FOLD, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE,
KEYWDS 2 RSGI, STRUCTURAL GENOMICS, LIGASE
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA,H.KAWAHARA,
AUTHOR 2 H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO,RIKEN STRUCTURAL
AUTHOR 3 GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 23-FEB-22 1IYF 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1IYF 1 VERSN
REVDAT 1 25-MAR-03 1IYF 0
JRNL AUTH E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA,
JRNL AUTH 2 S.YAMADA,H.KAWAHARA,H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA,
JRNL AUTH 3 K.KATO
JRNL TITL PARKIN BINDS THE RPN10 SUBUNIT OF 26S PROTEASOMES THROUGH
JRNL TITL 2 ITS UBIQUITIN-LIKE DOMAIN
JRNL REF EMBO REP. V. 4 301 2003
JRNL REFN ISSN 1469-221X
JRNL PMID 12634850
JRNL DOI 10.1038/SJ.EMBOR.EMBOR764
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1
REMARK 3 AUTHORS : BRUNGER (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 720 RESTRAINTS, 489 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 82
REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 129 RESIDUAL DIPOLAR COUPLING
REMARK 3 CONSTRAINTS, 20 DISTANCE RESTRAINTS FOR HYDROGEN BONDS.
REMARK 4
REMARK 4 1IYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-02.
REMARK 100 THE DEPOSITION ID IS D_1000005405.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303; 310
REMARK 210 PH : 6.0; 6.0
REMARK 210 IONIC STRENGTH : 0.3; 0.3
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.1MM PARKIN UBIQUITIN-LIKE
REMARK 210 DOMAIN U-15N, 13C; 50MM
REMARK 210 POTASSIUM PHOSPHATE BUFFER;
REMARK 210 0.1MM PARKIN UBIQUITIN-LIKE
REMARK 210 DOMAIN U-15N, 13C; 50MM
REMARK 210 POTASSIUM PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 2D_1H-COUPLED_
REMARK 210 1H-15N_HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.6, CNS 1.1
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-10
REMARK 465 RES C SSSEQI
REMARK 465 GLY A -4
REMARK 465 PRO A -3
REMARK 465 LEU A -2
REMARK 465 GLY A -1
REMARK 465 SER A 0
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O PHE A 7 H SER A 9 1.55
REMARK 500 O ILE A 44 O HIS A 68 2.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ASN A 8 69.22 -63.01
REMARK 500 1 HIS A 11 115.51 -160.52
REMARK 500 1 VAL A 17 154.60 177.10
REMARK 500 1 THR A 21 154.39 -37.18
REMARK 500 1 SER A 22 142.73 -18.26
REMARK 500 1 ILE A 23 -39.43 -39.70
REMARK 500 1 VAL A 30 -71.78 -58.46
REMARK 500 1 PRO A 37 -152.24 -65.17
REMARK 500 1 ALA A 38 -70.44 -106.54
REMARK 500 1 LEU A 41 -143.33 -82.67
REMARK 500 1 ALA A 46 36.28 23.62
REMARK 500 1 LEU A 50 87.81 -9.77
REMARK 500 1 VAL A 56 -133.45 -70.66
REMARK 500 1 CYS A 59 -78.66 -81.36
REMARK 500 1 ASP A 60 76.02 -168.73
REMARK 500 2 ASN A 8 68.90 -63.73
REMARK 500 2 VAL A 17 152.40 178.88
REMARK 500 2 THR A 21 150.58 -33.51
REMARK 500 2 SER A 22 142.99 -17.30
REMARK 500 2 ILE A 23 -39.99 -39.69
REMARK 500 2 VAL A 30 -73.41 -58.78
REMARK 500 2 PRO A 37 -148.87 -66.30
REMARK 500 2 ALA A 38 -68.02 -105.31
REMARK 500 2 GLN A 40 -76.31 -53.20
REMARK 500 2 LEU A 41 -138.36 -84.74
REMARK 500 2 ALA A 46 34.90 26.03
REMARK 500 2 LEU A 50 89.51 -14.52
REMARK 500 2 VAL A 56 -133.53 -82.29
REMARK 500 2 CYS A 59 -76.99 -96.71
REMARK 500 2 ASP A 60 76.65 -169.94
REMARK 500 3 ASN A 8 69.39 -63.91
REMARK 500 3 VAL A 17 157.59 175.41
REMARK 500 3 THR A 21 153.69 -35.19
REMARK 500 3 SER A 22 144.27 -16.62
REMARK 500 3 VAL A 30 -73.53 -61.88
REMARK 500 3 PRO A 37 -147.57 -67.04
REMARK 500 3 ALA A 38 -69.82 -105.96
REMARK 500 3 GLN A 40 -77.32 -49.02
REMARK 500 3 LEU A 41 -124.71 -81.94
REMARK 500 3 ALA A 46 37.86 26.87
REMARK 500 3 LEU A 50 107.64 -25.05
REMARK 500 3 VAL A 56 -135.01 -82.26
REMARK 500 3 CYS A 59 -79.10 -106.22
REMARK 500 3 ASP A 60 76.46 -165.39
REMARK 500 4 ASN A 8 68.53 -64.13
REMARK 500 4 VAL A 17 154.71 178.99
REMARK 500 4 THR A 21 152.42 -34.35
REMARK 500 4 SER A 22 143.14 -18.87
REMARK 500 4 VAL A 30 -74.01 -59.05
REMARK 500 4 PRO A 37 -145.19 -68.20
REMARK 500
REMARK 500 THIS ENTRY HAS 149 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5500 RELATED DB: BMRB
REMARK 900 5500 IS CHEMICAL SHIFT
REMARK 900 RELATED ID: MY_001000012.1 RELATED DB: TARGETDB
DBREF 1IYF A 1 76 UNP O60260 PRKN2_HUMAN 1 76
SEQADV 1IYF GLY A -4 UNP O60260 CLONING ARTIFACT
SEQADV 1IYF PRO A -3 UNP O60260 CLONING ARTIFACT
SEQADV 1IYF LEU A -2 UNP O60260 CLONING ARTIFACT
SEQADV 1IYF GLY A -1 UNP O60260 CLONING ARTIFACT
SEQADV 1IYF SER A 0 UNP O60260 CLONING ARTIFACT
SEQRES 1 A 81 GLY PRO LEU GLY SER MET ILE VAL PHE VAL ARG PHE ASN
SEQRES 2 A 81 SER SER HIS GLY PHE PRO VAL GLU VAL ASP SER ASP THR
SEQRES 3 A 81 SER ILE PHE GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN
SEQRES 4 A 81 GLY VAL PRO ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY
SEQRES 5 A 81 LYS GLU LEU ARG ASN ASP TRP THR VAL GLN ASN CYS ASP
SEQRES 6 A 81 LEU ASP GLN GLN SER ILE VAL HIS ILE VAL GLN ARG PRO
SEQRES 7 A 81 TRP ARG LYS
HELIX 1 1 SER A 22 GLN A 34 1 13
HELIX 2 2 VAL A 56 LEU A 61 1 6
SHEET 1 A 5 HIS A 11 VAL A 15 0
SHEET 2 A 5 ILE A 2 PHE A 7 -1 N VAL A 5 O PHE A 13
SHEET 3 A 5 GLN A 64 VAL A 70 1 O ILE A 69 N ARG A 6
SHEET 4 A 5 ARG A 42 PHE A 45 -1 N ARG A 42 O VAL A 70
SHEET 5 A 5 LYS A 48 GLU A 49 -1 O LYS A 48 N PHE A 45
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - b 23 2 Bytes